My opinion on late registration has varied over time. Used to hate it categorically, but now I believe that in the case of 10-30 minute or so late reg, it's a "necessary evil." Like, sometimes shit happens, you get home from work late, or maybe you forget that you were gonna play this tournament today, or maybe DST shenanigans just happened and when it starts isn't when you think it does. Used that way, it can give people chances to play who don't really truly deserve to be denied the tournament.
But in the case of some clients (I'm looking at YOU Carbon Poker) they extend it to absurd levels, like 2 1/2 to 3 HOURS, and that, to me, has a 100% negative impact on poker's metagame--in a game where metagaming is very, very important.
Me I think every one should start at the start. If they can't then they should not be allowed to registered late. But I also think that people that just sets out should be kicked out of the tourney has well.
People who are sitting out for more than minutes at a time ARE, for practical purposes, out of the tournament. I agree there should be some sort of penalization for people who build a monster stack and just leave for an hour or more then come back after the bubble burst or something. That's not good sportsmanship.